Showing papers in "Wiley Interdisciplinary Reviews: Computational Molecular Science in 2012"
TL;DR: An overview of the current possibilities of ORCA is provided and its efficiency is documents.
Abstract: ORCA is a general-purpose quantum chemistry program package that features virtually all modern electronic structure methods (density functional theory, many-body perturbation and coupled cluster theories, and multireference and semiempirical methods). It is designed with the aim of generality, extendibility, efficiency, and user friendliness. Its main field of application is larger molecules, transition metal complexes, and their spectroscopic properties. ORCA uses standard Gaussian basis functions and is fully parallelized. The article provides an overview of its current possibilities and documents its efficiency. © 2011 John Wiley & Sons, Ltd.
8,821 citations
TL;DR: Molpro (available at http://www.molpro.net) is a general-purpose quantum chemical program as discussed by the authors, which uses local approximations combined with explicit correlation treatments, highly accurate coupled-cluster calculations are now possible for molecules with up to approximately 100 atoms.
Abstract: Molpro (available at http://www.molpro.net) is a general-purpose quantum chemical program. The original focus was on high-accuracy wave function calculations for small molecules, but using local approximations combined with explicit correlation treatments, highly accurate coupled-cluster calculations are now possible for molecules with up to approximately 100 atoms. Recently, multireference correlation treatments were also made applicable to larger molecules. Furthermore, an efficient implementation of density functional theory is available.
2,999 citations
TL;DR: Natural bond orbital (NBO) methods encompass a suite of algorithms that enable fundamental bonding concepts to be extracted from Hartree-Fock (HF), Density Functional Theory (DFT), and post-HF computations as discussed by the authors.
Abstract: Natural bond orbital (NBO) methods encompass a suite of algorithms that enable fundamental bonding concepts to be extracted from Hartree-Fock (HF), Density Functional Theory (DFT), and post-HF computations. NBO terminology and general mathematical formulations for atoms and polyatomic species are presented. NBO analyses of selected molecules that span the periodic table illustrate the deciphering of the molecular wavefunction in terms commonly understood by chemists: Lewis structures, charge, bond order, bond type, hybridization, resonance, donor–acceptor interactions, etc. Upcoming features in the NBO program address ongoing advances in ab initio computing technology and burgeoning demands of its user community by introducing major new methods, keywords, and electronic structure system/NBO communication enhancements. © 2011 John Wiley & Sons, Ltd.
1,150 citations
TL;DR: The Psi4 program is a new approach to modern quantum chemistry, encompassing Hartree–Fock and density‐functional theory to configuration interaction and coupled cluster and offers flexible user input built on the Python scripting language that enables both new and experienced users to make full use of the program's capabilities.
Abstract: The Psi4 program is a new approach to modern quantum chemistry, encompassing Hartree–Fock and density-functional theory to configuration interaction and coupled cluster. The program is written entirely in C++ and relies on a new infrastructure that has been designed to permit high-efficiency computations of both standard and emerging electronic structure methods on conventional and high-performance parallel computer architectures. Psi4 offers flexible user input built on the Python scripting language that enables both new and experienced users to make full use of the program's capabilities, and even to implement new functionality with moderate effort. To maximize its impact and usefulness, Psi4 is available through an open-source license to the entire scientific community. © 2011 John Wiley & Sons, Ltd.
902 citations
TL;DR: In this review, a brief presentation of the main methodological and computational aspects of the polarizable continuum model will be given together with an analysis of strengths and critical issues of its coupling with different QM methods.
Abstract: The polarizable continuum model (PCM) is a computational method originally formulated 30 years ago but still today it represents one of the most successful examples among continuum solvation models. Such a success is mainly because of the continuous improvements, both in terms of computational efficiency and generality, made by all the people involved in the PCM project. The result of these efforts is that nowadays, PCM, with all its different variants, is the default choice in many computational codes to couple a quantum–mechanical (QM) description of a molecular system with a continuum description of the environment. In this review, a brief presentation of the main methodological and computational aspects of the method will be given together with an analysis of strengths and critical issues of its coupling with different QM methods. Finally, some examples of applications will be presented and discussed to show the potentialities of PCM in describing the effects of environments of increasing complexity. © 2012 John Wiley & Sons, Ltd.
681 citations
TL;DR: In this article, the authors focus on approximate spin-orbit coupling operators for practical use in molecular applications and review state-of-the-art theoretical methods for evaluating ISC rates.
Abstract: Many light-induced molecular processes involve a change in spin state and are formally forbidden in non-relativistic quantum theory. To make them happen, spin–orbit coupling (SOC) has to be invoked. Intersystem crossing (ISC), the nonradiative transition between two electronic states of different multiplicity, plays a key role in photochemistry and photophysics with a broad range of applications including molecular photonics, biological photosensors, photodynamic therapy, and materials science. Quantum chemistry has become a valuable tool for gaining detailed insight into the mechanisms of ISC. After a short introduction highlighting the importance of ISC and a brief description of the relativistic origins of SOC, this article focusses on approximate SOC operators for practical use in molecular applications and reviews state-of-the-art theoretical methods for evaluating ISC rates. Finally, a few sample applications are discussed that underline the necessity of studying the mechanisms of ISC processes beyond qualitative rules such as the El-Sayed rules and the energy gap law. © 2011 John Wiley & Sons, Ltd.
617 citations
TL;DR: The energy decomposition analysis (EDA) is a powerful method for a quantitative interpretation of chemical bonds in terms of three major components as discussed by the authors, which can be interpreted in chemically meaningful way thus providing a bridge between quantum chemical calculations and heuristic bonding models of traditional chemistry.
Abstract: The energy decomposition analysis (EDA) is a powerful method for a quantitative interpretation of chemical bonds in terms of three major components. The instantaneous interaction energy ΔEint between two fragments A and B in a molecule A–B is partitioned in three terms, namely (1) the quasiclassical electrostatic interaction ΔEelstat between the fragments; (2) the repulsive exchange (Pauli) interaction ΔEPauli between electrons of the two fragments having the same spin, and (3) the orbital (covalent) interaction ΔEorb which comes from the orbital relaxation and the orbital mixing between the fragments. The latter term can be decomposed into contributions of orbitals with different symmetry which makes it possible to distinguish between σ, π, and δ bonding. After a short introduction into the theoretical background of the EDA we present illustrative examples of main group and transition metal chemistry. The results show that the EDA terms can be interpreted in chemically meaningful way thus providing a bridge between quantum chemical calculations and heuristic bonding models of traditional chemistry. The extension to the EDA–Natural Orbitals for Chemical Valence (NOCV) method makes it possible to breakdown the orbital term ΔEorb into pairwise orbital contributions of the interacting fragments. The method provides a bridge between MO correlations diagrams and pairwise orbital interactions, which have been shown in the past to correlate with the structures and reactivities of molecules. There is a link between frontier orbital theory and orbital symmetry rules and the quantitative charge- and energy partitioning scheme that is provided by the EDA–NOCV terms. The strength of the pairwise orbital interactions can quantitatively be estimated and the associated change in the electronic structure can be visualized by plotting the deformation densities.
For further resources related to this article, please visit the WIREs website.
616 citations
TL;DR: In this article, the symmetry-adapted perturbation theory (SAPT) is used to predict and understand the structure and properties of clusters and condensed phase, and the broadest range of such predictions can be achieved by constructing potential energy surfaces from a set of SAPT interaction energies and using these surfaces in nuclear dynamics calculations.
Abstract: Basic concepts and most recent developments of symmetry-adapted perturbation theory (SAPT) are described. In particular, the methods that combine SAPT with density-functional theory are discussed. It is explained how SAPT allows one to predict and understand the structure and properties of clusters and condensed phase. The broadest range of such predictions can be achieved by constructing potential energy surfaces from a set of SAPT interaction energies and using these surfaces in nuclear dynamics calculations. © 2011 John Wiley & Sons, Ltd.
438 citations
TL;DR: In this paper, a review of recent works in wavefunction-based quantum chemistry techniques aimed at greater accuracy and faster computations for non-covalent interactions is presented, and a variety of wavefunction methods with promise for noncovalant interactions, various approximations to speed up these methods, and recent advances in wave function-based symmetry-adapted perturbation theory, which provides not only interaction energies but also their decomposition into physically meaningful components.
Abstract: Noncovalent interactions remain poorly understood despite their importance to supramolecular chemistry, biochemistry, and materials science. They are an ideal target for theoretical study, where interactions of interest can be probed directly, free from competing secondary interactions. However, the most popular tools of computational chemistry are not particularly reliable for noncovalent interactions. Here we review recent works in wavefunction-based quantum chemistry techniques aimed at greater accuracy and faster computations for these systems. We describe recent developments in high-accuracy benchmarks, a variety of recent wavefunction methods with promise for noncovalent interactions, various approximations to speed up these methods, and recent advances in wavefunction-based symmetry-adapted perturbation theory, which provides not only interaction energies but also their decomposition into physically meaningful components. Together, these advances are currently extending robust, accurate computations of noncovalent interactions from systems with around one dozen heavy atoms up to systems with several dozens of heavy atoms. © 2011 John Wiley & Sons, Ltd.
361 citations
TL;DR: This brief overview of coupled‐cluster theory will describe formal aspects of the theory which should be understood by perspective users of CC methods and comment on some current developments that are improving the theory's accuracy or applicability.
Abstract: Coupled-cluster theory offers today's reference quantum chemical method for most of the problems encountered in electronic structure theory. It has been instrumental in establishing the now well-known paradigm of converging, many-body methods,
Many-body perturbation theory (MBPT) for second, MBPT2, and fourth-order MBPT4; and coupled-cluster (CC) theory for different categories of excitations, singles, doubles, triples, quadruples (SDTQ). Although built on the same basic concept as configuration interaction (CI), many-body methods fundamentally improve upon CI approximations by introducing the property of size extensivity, meaning that contrary to any truncated CI all terms properly scale with the number of electrons in the problem. This fundamental aspect of many-electron methods leads to the exceptional performance of CC theory and its finite-order MBPT approximations plus its equation-of-motion extensions for excited, ionized, and electron attached states. This brief overview will describe formal aspects of the theory which should be understood by perspective users of CC methods. We will also comment on some current developments that are improving the theory's accuracy or applicability. © 2011 John Wiley & Sons, Ltd.
301 citations
TL;DR: The multiconfiguration time-dependent Hartree (MCTDH) method is a powerful and general algorithm for solving the timedependent Schr¨ odinger equation as discussed by the authors, which has been applied in many applications.
Abstract: This review covers the multiconfiguration time-dependent Hartree (MCTDH) method, which is a powerful and general algorithm for solving the timedependent Schr¨ odinger equation. The formal derivation is discussed as well as applications of the method. Recent extensions of MCTDH are treated in brief, namely, MCTDHB and MCTDHF, for treating identical particles (bosons and fermions), and the very powerful multilayer (ML-MCTDH) formalism. Compact representations of potential energy surfaces (PESs) are also discussed, as the representation of a PES becomes a major bottleneck when going to larger systems (nine or more dimensions) while employing a full-dimensional, complicated, and nonseparable PES. As applications of MCTDH, we discuss the calculation of photoionization and photoexcitation spectra of the vibronically coupled systems butatriene and pyrazine, respectively, and the infra-red spectrum of the Zundel cation (protonated water dimer) H5O + . C � 2011 John Wiley & Sons, Ltd.
TL;DR: Spin component-scaled (SCS) electron correlation methods for electronic structure theory can be derived theoretically by applying special conditions to the underlying wave functions in perturbation theory as mentioned in this paper, based on the insight that low-order wave function expansions treat the correlation effects of electron pairs with opposite spin (OS) and same spin (SS) differently.
Abstract: Spin-component-scaled (SCS) electron correlation methods for electronic structure theory are reviewed The methods can be derived theoretically by applying special conditions to the underlying wave functions in perturbation theory They are based on the insight that low-order wave function expansions treat the correlation effects of electron pairs with opposite spin (OS) and same spin (SS) differently because of their different treatment at the underlying Hartree–Fock level Physically, this is related to the different average inter-electronic distances in the SS and OS electron pairs The overview starts with the original SCS-MP2 method and discusses its strengths and weaknesses and various ways to parameterize the scaling factors Extensions to coupled-cluster and excited state methods as well the connection to virtual-orbital dependent density functional approaches are highlighted The performance of various SCS methods in large thermochemical benchmarks and for excitation energies is discussed in comparison with other common electronic structure methods
TL;DR: The density functional tight-binding (DFTB) method as discussed by the authors is based on the density functional theory as formulated by Hohenberg and Kohn, and it introduces several approximations: first, densities and potentials are written as superpositions of atomic densities.
Abstract: In this paper, we review the foundations of the density-functional tight-binding (DFTB) method. The method is based on the density-functional theory as formulated by Hohenberg and Kohn. It introduces several approximations: First, densities and potentials are written as superpositions of atomic densities and potentials. Second, many-center terms are summarized together with nuclear repulsion energy terms in a way that they can be written as a sum of pairwise repulsive terms. For small distances, the nuclear repulsion dominates, whereas for large distances, these terms vanish. The Kohn–Sham orbitals are expanded in a set of localized atom-centered functions. They are represented in a minimal basis of optimized atomic orbitals, which are obtained for spherical symmetric spin-unpolarized neutral atoms self-consistently. The whole Hamilton and overlap matrices contain one- and two-center contributions only. Therefore, they can be calculated and tabulated in advance as functions of the distance between atomic pairs. In addition, we discuss a self-consistent charge extension, the treatment of weak interactions, and a linear response scheme in connection with the DFTB method. Finally, some practical aspects are presented. © 2012 John Wiley & Sons, Ltd.
TL;DR: The ONIOM (our own n-layer integrated molecular orbital molecular mechanics) method is one of the most popular, successful, and easily-to-implement hybrid quantum mechanics/molecular mechanics (QM/MM) methods to treat complex molecular systems as discussed by the authors.
Abstract: The ONIOM (our Own N-layer Integrated molecular Orbital molecular Mechanics) method is one of the most popular, successful, and easily-to-implement hybrid quantum mechanics/molecular mechanics (QM/MM) methods to treat complex molecular systems. Hybrid QM/MM methods take advantage of the high accuracy of QM methods and the low computational cost of MM methods. One key feature of the ONIOM method is a simple linear extrapolation procedure, which allows the ONIOM method to be further extended to two-layer ONIOM(QM1:QM2), three-layer ONIOM(QM1:QM2:MM), and, in principle, any n-layer n-level-of-theory methods. Such hierarchical features of the ONIOM method are unique among the hybrid QM/MM methods. This review article provides an overview of the theoretical foundation and recent development of the ONIOM method. Some of its recent applications to metalloenzymes and photobiology will also be highlighted. Prospective ONIOM development for more realistic simulations on the complex systems will be discussed finally. © 2011 John Wiley & Sons, Ltd.
TL;DR: The objective of the present review is to provide an up‐to‐date overview of the CHARMM FFs, including underlying methodologies and principles, along with a brief description of the strategies used for parameter development.
Abstract: Empirical force fields commonly used to describe the condensed phase properties of complex systems such as biological macromolecules are continuously being updated. Improvements in quantum mechanical (QM) methods used to generate target data, availability of new experimental target data, incorporation of new classes of compounds and new theoretical developments (eg. polarizable methods) make force-field development a dynamic domain of research. Accordingly, a number of improvements and extensions of the CHARMM force fields have occurred over the years. The objective of the present review is to provide an up-to-date overview of the CHARMM force fields. A limited presentation on the historical aspects of force fields will be given, including underlying methodologies and principles, along with a brief description of the strategies used for parameter development. This is followed by information on the CHARMM additive and polarizable force fields, including examples of recent applications of those force fields.
TL;DR: In this paper, the authors propose the energetic span model, which is a bridge connecting the kinetic outcome of experimental and theoretical catalysis, and demonstrate the utility of working with Gibbs energies instead of the rate constants (k-representation), in line with the assertion that there are no rate determining steps, but rate-determining states.
Abstract: The energetic span model is a bridge connecting the kinetic outcome of experimental and theoretical catalysis. It proves the utility of working with Gibbs energies (E-representation) instead of the rate constants (k-representation), in line with the assertion saying that ‘there are no rate-determining steps, but rate-determining states’. With this model the turnover frequency (TOF), turnover number (TON) and the kinetic determining factors can be obtained from the reaction profile of a computed catalytic cycle. In this way, it is possible to examine, explain, and predict the efficiency of a catalyst. The effect of concentrations, different pathways, preactivation and deactivation, and the comparison of catalysts and reactants are analyzed with several examples from the literature. In addition, the AUTOF program (excel version) is presented, allowing the fast and simple analysis of theoretically calculated catalytic reactions. © 2012 John Wiley & Sons, Ltd.
TL;DR: The multiconfiguration second-order perturbation theory based on complete active space reference wave function (CASSCF/CASPT2) was proposed in this article.
Abstract: Rooted in the very fundamental aspects of many chemical phenomena, and for the majority of photochemistry, is the onset of strongly interacting electronic configurations. To describe this challenging regime of strong electron correlation, an extraordinary effort has been put forward by a young generation of scientists in the development of theories 'beyond' standard wave function and density functional models. Despite their encouraging results, a twenty-and-more-year old approach still stands as the gold standard for these problems: multiconfiguration second-order perturbation theory based on complete active space reference wave function (CASSCF/CASPT2). We will present here a brief overview of the CASSCF/CASPT2 computational protocol, and of its role in our understanding of chemical and photochemical processes.
TL;DR: In this article, a review of coupled cluster (CC) theory for electronic excited states is presented, and the basics of a CC response theory framework that allows the transfer of the attractive accuracy and convergence properties associated with CC methods over to the calculation of electronic excitation energies and properties.
Abstract: We review coupled cluster (CC) theory for electronically excited states. We outline the basics of a CC response theory framework that allows the transfer of the attractive accuracy and convergence properties associated with CC methods over to the calculation of electronic excitation energies and properties. Key factors affecting the accuracy of CC excitation energy calculations are discussed as are some of the key CC models in this field. To aid both the practitioner as well as the developer of CC excited state methods, we also briefly discuss the key computational steps in a working CC response implementation. Approaches aimed at extending the application range of CC excited state methods either in terms of molecular size and phenomena or in terms of environment (solution and proteins) are also discussed. © 2011 John Wiley & Sons, Ltd.
TL;DR: In this paper, the R12 ansatze has been applied to MP2, coupled-cluster, and equation of motion (EoM) theories, and the rational generator is used to create the exact cusp conditions (SP ansatz).
Abstract: Fundamental aspects of the explicitly correlated R12 and F12 theories are summarized in the perspective of recent advances related to our contribution in this field. Starting from the basics of pair functions and second quantized formulations, the R12/F12 ansatze have been applied to MP2, coupled-cluster, and equation of motion coupled-cluster theories. Emphasis is given to approaches that use the rational generator to create the exact cusp conditions (SP ansatz). Computational aspects of the evaluation of many-electron integrals are also discussed in conjunction with the use of the Slater-type geminal, which is the predominant choice for the correlation factor in modern R12/F12 theories. © 2011 John Wiley & Sons, Ltd.
TL;DR: This work focuses on the progress made in the development of more general and powerful collective variables and on the very recent and exciting evolutions of the metadynamics method.
Abstract: Metadynamics is an algorithm for accelerating rare events and reconstructing the associated free energy surface. It works by biasing the evolution of the system by a history-dependent potential that is adaptively constructed in the space of a suitably chosen set of collective variables. Since its first appearance, the method has been successfully applied in several domains of science. Its widespread adoption is not only due to its efficiency, flexibility, and availability but also to its continuous evolution and its combination with complementary enhanced sampling algorithms. Here, we focus on the progress made in the development of more general and powerful collective variables and on the very recent and exciting evolutions of the method. © 2012 John Wiley & Sons, Ltd.
TL;DR: The Born-Oppenheimer (BO) method as discussed by the authors is based on the same basic principles and can be derived from the same Lagrange function as the Car-Parrinello (CP) method.
Abstract: The Car–Parrinello (CP) method made molecular dynamics simulation with on-the-fly computation of interaction potentials from electronic structure theory computationally feasible. The method reformulates ab initio molecular dynamics (AIMD) as a two-component classical dynamical system. This approach proved to be valuable far beyond the original CP molecular dynamics method. The modern formulation of Born–Oppenheimer (BO) dynamics is based on the same basic principles and can be derived from the same Lagrange function as the CP method. These time-reversible BO molecular dynamics methods allow higher accuracy and efficiency while providing similar longtime stability as the CP method. AIMD is used in many fields of computational physics and chemistry. Its applications are instrumental in fields as divers as enzymatic catalysis and the study of the interior of planets. With its versatility and predictive power, AIMD has become a major approach in atomistic simulations. © 2011 John Wiley & Sons, Ltd.
TL;DR: Douglas-Kroll-Hess theory as discussed by the authors can be used to decouple positive and negative energy eigenstates of the Dirac one-electron Hamiltonian by an expansion in the external potential.
Abstract: Relativistic effects on molecular properties and energies are ubiquitous in chemistry. Their consideration in quantum chemical calculations requires Dirac's theory of the electron, whose application is not without obstacles. Douglas–Kroll–Hess theory accomplishes a decoupling of positive- and negative-energy eigenstates of the Dirac one-electron Hamiltonian by an expansion in the external potential. At low orders, this expansion already converges and provides efficient relativistic Hamiltonians to be used in routine quantum chemical calculations. The basic principles of the approach are reviewed, and most recent developments are discussed. © 2011 John Wiley & Sons, Ltd.
TL;DR: An overview ofCollective coordinates, as obtained by a principal component analysis of atomic fluctuations, are commonly used to predict a low‐dimensional subspace in which essential protein motion is expected to take place.
Abstract: Collective coordinates, as obtained by a principal component analysis of atomic fluctuations, are commonly used to predict a low-dimensional subspace in which essential protein motion is expected to take place. The definition of such an essential subspace allows to characterize protein functional, and folding, motion, to provide insight into the (free) energy landscape, and to enhance conformational sampling in molecular dynamics simulations. Here, we provide an overview on the topic, giving particular attention to some methodological aspects, such as the problem of convergence, and mentioning possible new developments. (c) 2012 John Wiley & Sons, Ltd.
TL;DR: A review of the most popular methods for electronic circular dichroism calculation can be found in this paper, focusing on time-dependent density functional theory, where the authors explain the origin of ECD and optical activity using response theory.
Abstract: First-principles calculations of electronic circular dichroism (ECD) are widely used to determine absolute configurations of chiral molecules. In addition, ECD is a sensitive probe for the three-dimensional molecular structure, making ECD calculations a useful tool to study conformational changes. In this review, we explain the origin of ECD and optical activity using response theory. While the quantum-mechanical underpinnings of ECD have been known for a long time, efficient electronic structure methods for ECD calculations on molecules with more than 10–20 atoms have become widely available only in the past decade. We review the most popular methods for ECD calculation, focusing on time-dependent density functional theory. Although single-point vertical ECD calculations yield useful accuracy for conformationally rigid systems, inclusion of finite-temperature effects is necessary for flexible molecules. The scope and limitations of modern ECD calculations are illustrated by applications to helicenes, fullerenes, iso-schizozygane alkaloids, paracyclophanes, β-lactams, and transition metal complexes. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 00 1–17 DOI: 10.1002/wcms.55
TL;DR: The chemical space of molecules following simple rules of chemical stability and synthetic feasibility has been enumerated up to 13 atoms of C, N, O, Cl, S, forming the GDB‐13 database with 977 million structures, which is organized in a 42‐dimensional chemical space using molecular quantum numbers (MQN) as descriptors.
Abstract: In the field of medicinal chemistry, the chemical space describes the ensemble of all organic molecules to be considered when searching for new drugs (estimated >1060 molecules), as well as the property spaces in which these molecules are placed for the sake of describing them. Molecules can be enumerated computationally by the millions, which was first undertaken in the field of computer-aided structure elucidation. Scoring the enumerated virtual libraries by virtual screening has recently become an attractive strategy to prioritize compounds for synthesis and testing. Enumeration methods include combinatorial linking of fragments, genetic algorithms based on cycles of enumeration and selection by ligand-based or target-based scoring functions, and exhaustive enumeration from first principles. The chemical space of molecules following simple rules of chemical stability and synthetic feasibility has been enumerated up to 13 atoms of C, N, O, Cl, S, forming the GDB-13 database with 977 million structures. The database has been organized in a 42-dimensional chemical space using molecular quantum numbers (MQN) as descriptors, which can be visualized by projection in two dimensions by principal component analysis, and searched within seconds using a Web browser available at www.gdb.unibe.ch. © 2012 John Wiley & Sons, Ltd.
TL;DR: The history of carbohydrate force fields is reviewed, examining and comparing their challenges, forms, philosophies, and development strategies, and a survey of recent uses is presented, noting trends, strengths, deficiencies, and possible directions for future expansion.
Abstract: Carbohydrates present a special set of challenges to the generation of force fields. First, the tertiary structures of monosaccharides are complex merely by virtue of their exceptionally high number of chiral centers. In addition, their electronic characteristics lead to molecular geometries and electrostatic landscapes that can be challenging to predict and model. The monosaccharide units can also interconnect in many ways, resulting in a large number of possible oligosaccharides and polysaccharides, both linear and branched. These larger structures contain a number of rotatable bonds, meaning they potentially sample an enormous conformational space. This article briefly reviews the history of carbohydrate force fields, examining and comparing their challenges, forms, philosophies, and development strategies. Then it presents a survey of recent uses of these force fields, noting trends, strengths, deficiencies, and possible directions for future expansion.
TL;DR: Density functional theory and density functional theory/molecular mechanics (DFT/MM) methods have been applied to the characterization of full catalytic cycles, as those in cross-coupling, to the systematic analysis of single reaction steps common to several catalytic cycle, such as CH activation, and to the elucidation of processes involving different spin states such as the rebound mechanism for CH activation as mentioned in this paper.
Abstract: Density functional theory (DFT) and density functional theory/molecular mechanics (DFT/MM) methods are useful tools in modern homogeneous catalysis. Calculation, with its ability to characterize otherwise hardly accessible intermediates and transition states, is a key complement to experiment for the full characterization of the often intricate reaction mechanisms involved in transition metal catalysis. DFT and DFT/MM techniques have been applied to the characterization of full catalytic cycles, as those in cross-coupling; to the systematic analysis of single reaction steps common to several catalytic cycles, such as CH activation; to the elucidation of processes involving different spin states, such as the rebound mechanism for CH activation; to the identification of transient intermediates with key mechanistic roles, such as those in oxygen-evolving complexes; to the analysis of the catalytic keys to polymerization control, as in olefin polymerization; and to reproduction and rationalization of experimentally reported enantioselectvities, as in the case of olefin dihydroxylation. The currently available techniques provide sufficient accuracy to offer chemical insight into the systems involved in experiment, as proved by the growing body of successful applications in the field. © 2012 John Wiley & Sons, Ltd.
TL;DR: This review compares and contrasts the diverse approaches taken by selected programs in both the design and implementation of molecule feature perception and reaction rule representation, and it is argued that the progress achieved in this aspect paves the way to a deeper exploration of computer approaches to applying strategy and control in the synthesis problem.
Abstract: The discipline of retrosynthetic analysis is now just over 40 years old. From the earliest day, attempts were made to incorporate this approach into computer programs to test the extent in which chemical perception and synthetic thinking could be formalized. Despite pioneering research efforts, computer-aided synthetic analysis failed to achieve widespread routine use by chemists, which can be attributed in part to the difficulty of building the required high-quality retrosynthetic transform databases required for credible analyses. However, with the advent over the past 25 years of large comprehensive reaction databases, work on successfully automating the construction of reliable and comprehensive reaction rule databases is promising to revitalize research in this field. This review compares and contrasts the diverse approaches taken by selected programs in both the design and implementation of molecule feature perception and reaction rule representation, and we review the concepts of synthetic strategy selection, representation, and execution. In particular, we discuss the current work on automating the construction of reliable and comprehensive synthetic rule sets from available reaction databases in newer programs such as ARChem. We argue that the progress achieved in this aspect paves the way to a deeper exploration of computer approaches to applying strategy and control in the synthesis problem. © 2011 John Wiley & Sons, Ltd.
TL;DR: In this article, a review of recent efforts to introduce a refined hierarchy of isodesmic bond-separation reactions for use in thermochemical predictions and to quantify the degree of error cancellation that can be achieved.
Abstract: Achieving highly accurate thermochemical predictions from relatively low levels of electronic structure theory has long been a goal of computational chemistry. One route to such a goal is to exploit the systematic cancellation of errors. This approach was spearheaded by the Pople group in the 1970s with the introduction of isodesmic bond-separation reactions, and then extended by other groups to homodesmotic (HD) and hyperhomodesmotic reactions over the ensuing years. Unfortunately, the propagation of multiple, nonequivalent definitions of HD reactions, accompanied by a panoply of related reaction classes, has lead to a great deal of confusion. We review recent efforts to introduce a refined hierarchy of HD reactions for use in thermochemical predictions and to quantify the degree of error cancellation that can be achieved. Examples of the use of reactions from the HD hierarchy from the literature are presented, as are current limitations of this HD hierarchy for thermochemistry. Although the use of such error-balanced reactions are no longer mandatory for high-accuracy thermochemical predictions of small molecules, they still offer significant advantages in this context, and offer one route to accurate thermochemical predictions of larger molecules. © 2011 John Wiley & Sons, Ltd.
TL;DR: An anharmonic force field is defined as a higher-order Taylor-series expansion of the molecular potential energy surface (PES) around a reference geometry, usually chosen to be an equilibrium structure as mentioned in this paper.
Abstract: An anharmonic force field is defined as a higher-order Taylor-series expansion of the molecular potential energy surface (PES) around a reference geometry, usually chosen to be an equilibrium structure. Force field expansions provide excellent local approximations to PESs, one of the most important theoretical constructs of chemistry. This review deals principally with the definition and physical interpretation of anharmonic molecular force fields, their determination via techniques of electronic structure theory, their transformation among different rectilinear and curvilinear representations, and their utilization. Physical and technical factors leading to more precise and more accurate force fields are also discussed. © 2011 John Wiley & Sons, Ltd.